Always do it manually or semi-manually. Input A thru C (mostly use A as that puts in the stitch angles will digitizing, actually hate Input B, but I digress, input C had it's place, especially for Applique (which I never used the applique tool), just don't use tatami stitches with these tools, it never looks right (if know what you are looking at and depending on the design and substrate, can cause havoc on the substrate)) or Complex Fill if wanting to stick with semi manual. And do the overlaps yourself. Wilcom has a lot of great features compared to other software, but with any of them actually, the more one is depending on too much abstraction, that's where issues can happen.
If wanting to automate, set up your own templates that work well with your machines as well with your own density, push/pull comp settings etc for fabrics that you use most and only have to use the manual semi manual tools at that point. When I was doing this, I actually had templates that were already setup with some base objects as well (like if doing ornaments etc).
Most embroidery software have strong points, one may be strong in point A, but suck at Point B. In order to get Point B and not wanting to do it yourself, have to get software that does Point B great. Not really feasible (especially if you are already running a full version of Wilcom, Adobe would love to have that price structure I'm sure). Why I always suggest learn to do it yourself (and somethings still have to be done this way).